Fig. 1: scATAC-seq atlasing with commercial and improved custom technology.
From: Evaluating single-cell ATAC-seq atlasing technologies using sequence-to-function modeling
a Mouse cortex data were partly downloaded from the official 10x Genomics website and partly generated in-house. Overview of the sample generation: dissection of mouse motor cortex, tissue lysis, followed by droplet encapsulation for cell barcoding. For HyDrop v1, only one bead batch was generated (data reused from De Rop et al., 2022), while for HyDrop v2, seven bead batches were generated. b Drosophila melanogaster embryos were collected 16-20 h after egg laying. In-house experiments were performed with 10x v2 chemistry on the 10x Chromium device, while HyDrop v2 beads were used for the open-source data generation. sciATAC-seq3 data (plate-based essay) were retrieved from Calderon et al. (2022). c Comparison between bead barcoding chemistries of HyDrop v1 and v2. d The HyDrop v1 protocol was optimized in two ways: (1) the barcoding of the beads was changed from a cyclic polymerase extension to a linear ligation-based chemistry (right), and (2) Bead chemistry was adjusted in several optimization rounds (left). e Sanger sequencing of an exemplary HyDrop v1 bead (top) showing impurity in barcode one and barcode two, and a HyDrop v2 bead (bottom) with pure barcode signals across all three barcodes. f Estimation of generation costs of 67k cells in euros, excluding sequencing costs. Source data are provided as a Source Data file. HyDrop v1: 851.53 euro, HyDrop v2: 668.18 euro, 10x v2: 9,337.79 euro.
